Various representation learning methods for molecular structures have been devised to accelerate data-driven chemistry. However, the representation capabilities of existing methods are essentially limited to atom-level information, which is not sufficient to describe real-world molecular physics. Although electron-level information can provide fundamental knowledge about chemical compounds beyond the atom-level information, obtaining the electron-level information in real-world molecules is computationally impractical and sometimes infeasible. We propose a method for learning electron-informed molecular representations without additional computation costs by transferring readily accessible electron-level information about small molecules to large molecules of our interest. The proposed method achieved state-of-the-art prediction accuracy on extensive benchmark datasets containing experimentally observed molecular physics. The source code for HEDMoL is available at https://github.com/ngs00/HEDMoL.

Recently, molecular relational learning, whose goal is to predict the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. In this work, we propose CMRL that is robust to the distributional shift in molecular relational learning by detecting the core substructure that is causally related to chemical reactions. To do so, we first assume a causal relationship based on the domain knowledge of molecular sciences and construct a structural causal model (SCM) that reveals the relationship between variables. Based on the SCM, we introduce a novel conditional intervention framework whose intervention is conditioned on the paired molecule. With the conditional intervention framework, our model successfully learns from the causal substructure and alleviates the confounding effect of shortcut substructures that are spuriously correlated to chemical reactions. Extensive experiments on various tasks with real-world and synthetic datasets demonstrate the superiority of CMRL over state-of-the-art baseline models.

Graph neural networks (GNNs) have been widely studied as an efficient and generalized method to predict the physical and chemical properties of chemical systems based on a single homogeneous atomic structure, such as molecule and crystalline material. However, most chemical systems in real-world applications of materials science and engineering contain multiple heterogeneous atomic substructures. Nonetheless, existing GNNs for chemical applications assumed homogeneous graphs with the input node or edge features in the same feature space. In this paper, we reformulate the regression problem on chemical systems as a regression problem on core substructures conditioned by environment substructures. Then, we propose conditional atomic subgraph interaction network (CASIN) that predicts the physical and chemical properties of the input chemical systems by learning the atomic interactions between the heterogeneous core and environment substructures in the chemical systems. For three real-world benchmark chemical datasets, CASIN outperformed state-of-the-art GNNs in predicting the physical and chemical properties of the complex solar cell materials and catalyst systems.

Extrapolation to predict unseen data outside the training distribution is a common challenge in real-world scientific applications of physics and chemistry. However, the extrapolation capabilities of neural networks have not been extensively studied in machine learning. Although it has been recently revealed that neural networks become linear regression in extrapolation problems, a universally applicable method to support the extrapolation of neural networks in general regression settings has not been investigated. In this paper, we propose automated nonlinearity encoder (ANE) that is a data-agnostic embedding method to improve the extrapolation capabilities of neural networks by conversely linearizing the original input-to-target relationships without architectural modifications of prediction models. ANE achieved state-of-the-art extrapolation accuracies in extensive scientific applications of various data formats. As a real-world application, we applied ANE for high-throughput screening to discover novel solar cell materials, and ANE significantly improved the screening accuracy.

Feature extraction has been widely studied to find informative latent features and reduce the dimensionality of data. In particular, due to the difficulty in obtaining labeled data, unsupervised feature extraction has received much attention in data mining. However, widely used unsupervised feature extraction methods require side information about data or rigid assumptions on the latent feature space. Furthermore, most feature extraction methods require predefined dimensionality of the latent feature space,which should be manually tuned as a hyperparameter. In this article, we propose a new unsupervised feature extraction method called Unsupervised Subspace Extractor ( USE ), which does not require any side information and rigid assumptions on data. Furthermore, USE can find a subspace generated by a nonlinear combination of the input feature and automatically determine the optimal dimensionality of the subspace for the given nonlinear combination. The feature extraction process of USE is well justified mathematically, and we also empirically demonstrate the effectiveness of USE for several benchmark datasets.

With great growth in the volume of chemical databases, machine learning receives significant attention from various scientific communities for efficient high-throughput screening of molecular properties and drug discovery on the millions of chemical compounds. In particular, graph neural networks (GNNs) have been widely studied in chemistry-related fields because a molecule is natively represented as a mathematical graph. In GNNs for the graph-level analysis, a global operation called readout is applied after node embedding to generate a graph-level embedding that represents characteristics of the whole graph. However, commonly used readouts frequently distort scale information of the graph and consequently degrade the prediction accuracy of GNNs. This problem becomes more serious in molecular machine learning because molecules have many important scale information (e.g., molecular weight and total energy). In this paper, we investigate this scale distortion problem in GNNs caused by the readouts for the first time and propose an efficient solution with a new attention-based readout. In the experiments, the proposed readout outperformed commonly used readouts on various GNN architectures.

With precipitously growing demand to detect outliers in data streams, many studies have been conducted aiming to develop extensions of well-known outlier detection algorithm called Local Outlier Factor (LOF), for data streams. However, existing LOF-based algorithms for data streams still suffer from two inherent limitations: 1) Large amount of memory space is required. 2) A long sequence of outliers is not detected. In this paper, we propose a new outlier detection algorithm for data streams, called DILOF that effectively overcomes the limitations. To this end, we first develop a novel density-based sampling algorithm to summarize past data and then propose a new strategy for detecting a sequence of outliers. It is worth noting that our proposing algorithms do not require any prior knowledge or assumptions on data distribution. Moreover, we accelerate the execution time of DILOF about 15 times by developing a powerful distance approximation technique. Our comprehensive experiments on real-world datasets demonstrate that DILOF significantly outperforms the state-of-the-art competitors in terms of accuracy and execution time. The source code for the proposed algorithm is available at our website: http://di.postech.ac.kr/DILOF.